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The Enterprise responds to an urgent call from CaptainDonald Varley, an old friend of Captain Picard. Varley's ship, the USS Yamato, which is the sister ship of the Enterprise, has been plagued by a series of system malfunctions while near the Romulan Neutral Zone. Upon rendezvousing with the Enterprise, Varley explains to Picard that he was investigating "rumors...that started making the Iconians sound a lot less like legend" and had, in fact, located the planetIconia in the Neutral Zone.

As Varley continues, revealing his goal of preventing the Romulans from gaining Iconian technology, his transmission to the Enterprise cuts in and out. Worf detects a failure in the Yamato's antimatter containment chamber. Before the Enterprise crew can act, the Yamato explodes and all 1,000+ crew members are killed. Meanwhile, a Romulan warbird (D'deridex-class) enters the Enterprise's sensor range.

As the investigation continues, Picard searches through Captain Varley's personal log to more thoroughly understand his friend's intent, asking the computer to highlight the words "Romulan" and/or "Iconian" in the log. In the archived logs, Varley describes finding Iconian artifacts, locating their homeworld, a puzzling Iconian probe scan, and the increasingly dangerous systems failures affecting his ship. In his final entry, he is determined to convince Picard of the importance of this mission to the safety of the Federation.

Searching for clues

Picard's ready room door fails to immediately open as he approaches, the first sign of trouble on the Enterprise. The bridge crew observes a visual record of the Iconian probe scan mentioned in Varley's log, and Data determines the coordinates at which this event occurred. Picard decides to take the Enterprise to this planet, on the far side of the Neutral Zone, and assume the Yamato's mission. A mission that Picard believes will prevent a war.

Wesley Crusher talks privately with Captain Picard about the Iconians, who were remarkably technologically advanced and were rumored to be able to magically appear on planets throughout the galaxy. However, Picard sees through Wesley's cover and asks him what really brought him into Picard's ready room. Wesley confesses that he can't stop thinking about how all the people on the Yamato were just suddenly dead and he states he doesn't know how Picard and Riker and the others can handle that so easily. Picard reassures Wesley that they are able to handle it because they have been trained to do so, as Wesley will be. However, Picard starts to remark about how the death of a single individual fails to move them, then is interrupted by a malfunction in the replicator. Picard has ordered Earl Grey tea from the replicator, and instead of tea, a potted plant materializes. "Now that should not have happened," he remarks to Wesley.

"Stop, dammit!"

La Forge begins to suspect that the Iconian probe had something to do with the Yamato's destruction, but has no explanation for the apparently random problems being experienced on the Enterprise. Upon arrival at the Iconian homeworld, the Enterprise finds the planet largely destroyed from orbit approximately 200,000 years ago. One small energy signature remains, however, and soon a probe is launched toward the Enterprise.

Picard initially intends to capture the probe in a tractor beam, but a frantic La Forge, now aware of the imminent danger but unable to contact the bridge due to an intercom failure, takes a wild turbolift ride to the Bridge, being thrown all about the turbolift as it races through the turbolift shafts including being stuck at the top and bottom of the lift car. He is thrown about so violently that his VISOR is knocked off of his face. Upon arriving on the bridge, Geordi is literally thrown out of the turbolift and is assisted to his feet by Riker just in time to warn Picard to destroy the probe. Picard orders Worf to destroy the probe and after he does so, Geordi tells Picard that if the probe had successfully scanned the Enterprise, there would have been no chance of saving the ship.

In the observation lounge, La Forge explains that the Iconian probe was transmitting an alien computer program to rewrite software in its own image. That was the cause behind the Yamato's systems failures. The Enterprise was not scanned by the probe, but did download the Yamato's log before its destruction, and contained within the log was the alien program. This means the Enterprise has a little breathing room, but likely not enough.

"What happened!?"

As La Forge and Data work on correcting the problems, Picard realizes that information on the planet may be useful. He decides to lead an away team to the planet's surface – over Riker's objection – to find this information. As soon as Picard, Data, and Worfbeam down to the surface, a Romulan warbird decloaks in orbit near the Enterprise.

The Haakona attempts to fire photon torpedoes but appears to be experiencing problems similar to those of the Enterprise, leading Riker to conclude that they too have tapped into the Yamato log. When another probe is launched from Iconia, Riker informs Taris to destroy it, which she does. But because of the remaining Romulan threat, Riker wants the shields to stay up, meaning that the away team cannot return to the ship.

On the surface of Iconia, the away team cannot establish contact with the Enterprise. Picard and Data attempt to make sense of a large console in the Iconian control room. Data determines that the Iconian language shares enough common roots with other languages to enable him to develop a working understanding of the controls. This understanding proves to be somewhat less than working, as Data's attempts to engage "manual override" result in the appearance of a gateway. A series of landscapes and architectures cycles through the gateway.

Picard concludes that the Iconians traveled to distant worlds through this gateway "as easily as we would cross a room." This is what Captain Varley was investigating and hoping to keep out of Romulan hands. As the team continues to stare into the gateway, an image of the Enterprise bridge appears briefly, offering a potential means of return to the ship. Meanwhile, Data appears to gain access to an underground power source activated by the gateway's appearance, but as he works the controls, an energy surge similar to the Iconian probe's transmission cripples him.

Picard and Worf try to assist Data, but his software is being rewritten by the Iconian program. Picard realizes that he must destroy all the Iconian technology, and asks Data how to go about that. He also orders Worf to destroy his tricorder containing everything they have learned thus far about the Iconians to keep the information from getting into enemy hands. Deciphering Data's broken speech, Picard surmises that he can launch all the Iconian probes but override the launchbay doors, so that the backwash from the rockets spills into the power grids to create an overload. Data is able to give Picard the correct key sequence for launching the probes (blue-amber-amber-red) and for overriding the doors (blue-blue-blue). Picard orders Worf to take Data through the gateway the next time the Enterprise appears.

"You must get Data back to the Enterprise."

Worf arrives on the Enterprise with Data and takes him to Engineering. La Forge ascertains that all of Data's systems "are just going crazy" but cannot help him. He laments not having an expert on Soong-type androids such as Maddox on the Enterprise to help with Data. The beeping emanating from La Forge's tricorder turns into a continuous tone, and it appears that Data has died.

On Iconia, Picard presses "blue-amber-amber-red" on the console, waits a moment, then enters "blue-blue-blue".

In Engineering, Data's eyes suddenly open and he sits up, apparently fully functional. La Forge surmises that Data's self-correcting mechanism wiped all memory affected by the Iconian program in order to save him; this had required a "cold boot": thus why Data had briefly shut down and why he knows nothing of events since he was infected. La Forge proposes a similar procedure for the Enterprise: a complete shutdown, a wipe of all affected memory (including the Yamato logs), and then a reload of systems from the protected archives in the central computer core. Despite the risks of doing so while facing a Romulan warbird, Riker decides to proceed.

Wrong address

Picard appears to have been successful. Seeing that the control room itself will be destroyed in moments, he decides to go through the gateway rather than die on Iconia. As he approaches it, the scenery switches from a pristine planet to the bridge of the Haakona. Given the options, he quickly makes his decision.

The Iconian program has been successfully removed from the Enterprise's computer, and ChiefO'Brien searches for Picard on the planet. But as soon as the transporter locks onto him, Picard vanishes. O'Brien soon locates him on the warbird, where Picard learns that the Romulan's auto-destruct sequence is active and cannot be disengaged. When O'Brien beams him back to the Enterprise, Picard informs the Bridge to move the Enterprise away because of the impending explosion of the warbird, but Riker intervenes and offers Taris the solution to purging her computer systems.

Having succeeded in preventing war with the Romulans, the Enterprise leaves orbit of the now entirely barren Iconia, as explosions continue to detonate on the horizon. Eventually, the Haakona, apparently able to purge its systems, leaves as well.

"The risk would be allowing the Romulans to locate Iconia. Fortunately, I got there first. It's a virtually dead planet, but enough technology remains to give the Romulans an edge if they should find it."

"The knitter isn't working."
"Try a splint."
"Doctor?"
"Splint. It's a very ancient concept. You take two flat pieces of wood or plastic, a bandage. The broken limb is kept immobile."
"That's crazy! That's not practicing medicine!"
"Oh, yes it is! It's a time honored way to practice medicine: with your head, and your heart, and your hands. So jump to it."

- A nurse and Pulaski

(Data pulls La Forge away from a computer access panel that is shocking him, causing him to fly through the air and land on his face)
"Data?"
"Yes?"
"What happened?"
"Any answer would be mere speculation. This is yet another example of how our actions have random results."
"Thanks, Data... I noticed."

- Data and Geordi La Forge

"Sir, the shields are back up!"
"Impeccable timing."
"Sir, the shields are back down."

- Wesley Crusher to William T. Riker

"If it should become necessary to fight, could you arrange to find me some rocks to throw at them?"

- Riker, frustrated over the systems failures while facing down the IRW Haakona

"Fate: Protects fools, little children, and ships named Enterprise."

- Riker

"I have claimed this planet for the Romulan Empire."
"This is the Neutral Zone. No one can claim anything."
"You will withdraw, or I will be forced to destroy your ship and your Away Team!!"

- Taris and Riker

"In another time and place, this could be funny."

- Deanna Troi, on the system failures

"This would appear to be manual override."
(Data presses a button and a portal appears.)
"That was not...manual override."

- Data to Worf and Picard

"I am accessing!"

- Data, after apparently shutting down

"May I help?"

- Data, after a plan is formed from his very recent death and revival

"Do you wish to evacuate all non-essential personnel to the Enterprise, sir?"
"No, that'd be premature."

Picard uses his catch-phrase "Tea, Earl Grey, hot" for the first time. Ironically, he is not able to drink it, as the replicator gives him a potted plant rather than the tea.

This episode is the first in the series to mention Picard's interest in archaeology.

Geordi La Forge references Bruce Maddox in Engineering while trying to diagnose what is happening to Data.

This is the first episode where the number for the LCARS is not 40271. The number that appears is 40272.

A stock photograph of Toronto City Hall was viewed through the Iconian gateway as a possible destination for the Iconians. Due to the advanced age of the gateway, it seems unlikely that this photograph was intended to represent the Earth city.

Carolyn Seymour, who plays Romulan commander Taris in this episode, went on to play a different Romulan commander in TNG: "Face of the Enemy". According to the Companion, the production staff created a new character for her in the belief that Taris was likely dead.